HEADER APOPTOSIS/SIGNALING PROTEIN 20-MAR-12 2LR1 TITLE STRUCTURAL MECHANISM FOR BAX INHIBITION BY CYTOMEGALOVIRUS PROTEIN TITLE 2 VMIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BAX; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BCL-2-LIKE PROTEIN 4, BCL2-L-4; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: IMMEDIATE EARLY GLYCOPROTEIN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 130-150; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BAX, BCL2L4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 5; SOURCE 12 ORGANISM_TAXID: 10360; SOURCE 13 OTHER_DETAILS: STRAIN AD169 KEYWDS APOPTOSIS-SIGNALING PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.MA REVDAT 4 01-MAY-24 2LR1 1 REMARK REVDAT 3 22-FEB-17 2LR1 1 REMARK REVDAT 2 16-JAN-13 2LR1 1 JRNL REVDAT 1 05-DEC-12 2LR1 0 JRNL AUTH J.MA,F.EDLICH,G.A.BERMEJO,K.L.NORRIS,R.J.YOULE,N.TJANDRA JRNL TITL STRUCTURAL MECHANISM OF BAX INHIBITION BY CYTOMEGALOVIRUS JRNL TITL 2 PROTEIN VMIA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 20901 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 23213219 JRNL DOI 10.1073/PNAS.1217094110 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR, XPLOR REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (XPLOR), REMARK 3 SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (XPLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LR1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000102725. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.1 MM PROTEIN_1, 0.1 MM [U-100% REMARK 210 13C; U-100% 15N] PROTEIN_2, 20 REMARK 210 MM POTASSIUM PHOSPHATE, 5 M [U- REMARK 210 100% 2H] D2O, 50 M H2O, DTT, 90% REMARK 210 H2O/10% D2O; 0.1 MM [U-100% 15N] REMARK 210 PROTEIN_1, 0.1 MM PROTEIN_2, 20 REMARK 210 MM POTASSIUM PHOSPHATE, 5 M [U- REMARK 210 100% 2H] D2O, 50 M H2O, DTT, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H NOESY; 3D HNCO; 3D REMARK 210 HNCACB; 3D 1H-15N NOESY; 2D 1H- REMARK 210 13C HSQC; 3D 1H-13C NOESY; 2D REMARK 210 DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PRO A 13 H SER A 15 1.24 REMARK 500 O LEU A 148 H ILE A 152 1.42 REMARK 500 O GLU A 6 HB3 GLN A 7 1.55 REMARK 500 O SER A 15 HD11 ILE A 19 1.56 REMARK 500 OG1 THR A 167 HD2 PRO A 168 1.56 REMARK 500 OD1 ASP A 2 H GLY A 3 1.59 REMARK 500 O ARG A 147 N LEU A 149 1.79 REMARK 500 O PRO A 13 N SER A 15 2.15 REMARK 500 O ALA A 178 OG1 THR A 182 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 3 ASP A 2 CG ASP A 2 OD1 0.192 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 ASP A 2 CB - CG - OD1 ANGL. DEV. = 8.9 DEGREES REMARK 500 3 ASP A 2 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 5 ASP A 2 CB - CG - OD1 ANGL. DEV. = 9.4 DEGREES REMARK 500 5 ASP A 2 CB - CG - OD2 ANGL. DEV. = -15.9 DEGREES REMARK 500 13 ASP A 2 OD1 - CG - OD2 ANGL. DEV. = -12.5 DEGREES REMARK 500 13 ASP A 2 CB - CG - OD1 ANGL. DEV. = 10.1 DEGREES REMARK 500 14 LEU A 47 CA - C - O ANGL. DEV. = -13.6 DEGREES REMARK 500 16 ASP A 2 CB - CG - OD1 ANGL. DEV. = -8.8 DEGREES REMARK 500 16 PRO A 168 N - CD - CG ANGL. DEV. = 9.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 SER A 4 -22.68 -152.53 REMARK 500 1 GLN A 7 66.98 97.04 REMARK 500 1 PRO A 8 -138.43 -51.87 REMARK 500 1 THR A 14 43.16 -46.74 REMARK 500 1 SER A 15 -148.69 -47.65 REMARK 500 1 LEU A 25 -81.03 -86.99 REMARK 500 1 LEU A 26 -65.88 -26.57 REMARK 500 1 GLN A 28 -18.04 -47.28 REMARK 500 1 PHE A 30 -18.86 -42.15 REMARK 500 1 GLN A 32 30.16 -78.85 REMARK 500 1 ALA A 42 72.00 69.96 REMARK 500 1 LEU A 47 -72.72 175.74 REMARK 500 1 GLN A 52 -72.25 -74.88 REMARK 500 1 ASP A 84 161.69 -41.06 REMARK 500 1 SER A 87 86.31 -175.94 REMARK 500 1 PHE A 100 57.60 -111.18 REMARK 500 1 ASP A 102 -18.30 -155.60 REMARK 500 1 ASN A 104 34.42 174.50 REMARK 500 1 PHE A 105 29.15 42.60 REMARK 500 1 ASN A 106 -110.43 -52.20 REMARK 500 1 TRP A 107 -26.15 174.55 REMARK 500 1 LYS A 128 46.44 85.14 REMARK 500 1 ARG A 147 -110.85 -142.28 REMARK 500 1 LEU A 148 -27.72 -15.42 REMARK 500 1 PHE A 165 48.13 -71.66 REMARK 500 1 PRO A 168 -145.69 -71.45 REMARK 500 1 THR A 169 102.22 -23.39 REMARK 500 1 GLN A 171 -14.35 -47.16 REMARK 500 1 PHE A 176 -60.05 -94.65 REMARK 500 1 LYS A 189 128.28 -175.74 REMARK 500 1 ALA B 132 120.86 51.83 REMARK 500 1 LYS B 134 24.32 48.83 REMARK 500 1 LYS B 135 75.12 -161.67 REMARK 500 1 ALA B 136 9.20 -172.45 REMARK 500 1 LEU B 137 -81.08 -84.47 REMARK 500 1 ARG B 141 -32.44 -34.24 REMARK 500 1 ARG B 146 -81.92 51.91 REMARK 500 1 ARG B 149 76.38 51.49 REMARK 500 2 GLN A 7 25.57 99.83 REMARK 500 2 PRO A 13 -70.74 -47.62 REMARK 500 2 THR A 14 74.81 -20.27 REMARK 500 2 SER A 15 -153.24 -128.83 REMARK 500 2 LEU A 25 -80.87 -86.93 REMARK 500 2 LEU A 26 -65.93 -26.75 REMARK 500 2 GLN A 28 -18.12 -47.36 REMARK 500 2 PHE A 30 -18.83 -42.23 REMARK 500 2 GLN A 32 30.04 -79.00 REMARK 500 2 GLU A 41 -139.32 44.76 REMARK 500 2 PRO A 43 155.10 -46.52 REMARK 500 2 LEU A 47 143.04 109.99 REMARK 500 REMARK 500 THIS ENTRY HAS 758 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 1 ASP A 2 7 -146.60 REMARK 500 GLY A 3 SER A 4 7 -119.27 REMARK 500 SER A 4 GLY A 5 7 126.52 REMARK 500 GLY A 5 GLU A 6 7 125.17 REMARK 500 GLN A 7 PRO A 8 7 122.13 REMARK 500 PRO A 8 ARG A 9 7 118.95 REMARK 500 ARG A 9 GLY A 10 7 122.57 REMARK 500 GLY A 10 GLY A 11 7 133.31 REMARK 500 GLY A 11 GLY A 12 7 -144.30 REMARK 500 GLY A 12 PRO A 13 7 -105.84 REMARK 500 THR A 14 SER A 15 7 -149.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 3 ASP A 2 0.10 SIDE CHAIN REMARK 500 5 ASP A 2 0.11 SIDE CHAIN REMARK 500 16 ASP A 2 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 14 LEU A 47 14.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F16 RELATED DB: PDB REMARK 900 RELATED ID: 18340 RELATED DB: BMRB DBREF 2LR1 A 1 192 UNP Q07812 BAX_HUMAN 1 192 DBREF 2LR1 B 130 150 UNP P16778 VGLI_HCMVA 130 150 SEQRES 1 A 192 MET ASP GLY SER GLY GLU GLN PRO ARG GLY GLY GLY PRO SEQRES 2 A 192 THR SER SER GLU GLN ILE MET LYS THR GLY ALA LEU LEU SEQRES 3 A 192 LEU GLN GLY PHE ILE GLN ASP ARG ALA GLY ARG MET GLY SEQRES 4 A 192 GLY GLU ALA PRO GLU LEU ALA LEU ASP PRO VAL PRO GLN SEQRES 5 A 192 ASP ALA SER THR LYS LYS LEU SER GLU CYS LEU LYS ARG SEQRES 6 A 192 ILE GLY ASP GLU LEU ASP SER ASN MET GLU LEU GLN ARG SEQRES 7 A 192 MET ILE ALA ALA VAL ASP THR ASP SER PRO ARG GLU VAL SEQRES 8 A 192 PHE PHE ARG VAL ALA ALA ASP MET PHE SER ASP GLY ASN SEQRES 9 A 192 PHE ASN TRP GLY ARG VAL VAL ALA LEU PHE TYR PHE ALA SEQRES 10 A 192 SER LYS LEU VAL LEU LYS ALA LEU CYS THR LYS VAL PRO SEQRES 11 A 192 GLU LEU ILE ARG THR ILE MET GLY TRP THR LEU ASP PHE SEQRES 12 A 192 LEU ARG GLU ARG LEU LEU GLY TRP ILE GLN ASP GLN GLY SEQRES 13 A 192 GLY TRP ASP GLY LEU LEU SER TYR PHE GLY THR PRO THR SEQRES 14 A 192 TRP GLN THR VAL THR ILE PHE VAL ALA GLY VAL LEU THR SEQRES 15 A 192 ALA SER LEU THR ILE TRP LYS LYS MET GLY SEQRES 1 B 21 CYS GLU ALA LEU LYS LYS ALA LEU ARG ARG HIS ARG PHE SEQRES 2 B 21 LEU TRP GLN ARG ARG GLN ARG ALA HELIX 1 1 SER A 16 ALA A 35 1 20 HELIX 2 2 ASP A 53 ASP A 71 1 19 HELIX 3 3 ASN A 73 VAL A 83 1 11 HELIX 4 4 SER A 87 PHE A 100 1 14 HELIX 5 5 GLY A 108 LYS A 128 1 21 HELIX 6 6 VAL A 129 ARG A 147 1 19 HELIX 7 7 LEU A 148 GLN A 155 1 8 HELIX 8 8 TRP A 158 PHE A 165 1 8 HELIX 9 9 THR A 169 VAL A 173 5 5 HELIX 10 10 ILE A 175 LYS A 189 1 15 HELIX 11 11 LEU B 137 ARG B 146 1 10 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1